hmmm.. i have had that situation when i overload my machine. do you think you might be getting close to max memory when this happens? (max memory == starting to swap to disk more.. hitting the page file)

a side note: why not make the main full screen and adjust the clones so they are vertical centered but still the same aspect ratio? it might look nicer on your main.

and depending on your play style, if you find you don't go to your clones very often, how about shrinking them a bit, taking up less room, and just pip swapping when you need them? the smaller size would radically drop the pixels/sec pushed from them to the graphics card.. .leaving more for your main and pip-swap